Multiple sequence alignment - TraesCS4D01G215400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G215400 chr4D 100.000 6356 0 0 1 6356 369111581 369117936 0.000000e+00 11738.0
1 TraesCS4D01G215400 chr4D 79.442 394 48 15 5785 6151 449913827 449913440 1.370000e-61 248.0
2 TraesCS4D01G215400 chr4A 94.616 3083 87 31 598 3632 95382685 95379634 0.000000e+00 4700.0
3 TraesCS4D01G215400 chr4A 94.669 2776 87 19 3630 6356 95379511 95376748 0.000000e+00 4250.0
4 TraesCS4D01G215400 chr4A 87.225 454 36 12 93 545 95383222 95382790 1.230000e-136 497.0
5 TraesCS4D01G215400 chr4A 90.090 111 7 3 2 110 95383343 95383235 2.390000e-29 141.0
6 TraesCS4D01G215400 chr4B 89.510 2469 154 50 71 2489 454513031 454515444 0.000000e+00 3027.0
7 TraesCS4D01G215400 chr4B 90.821 2179 140 37 2769 4922 454515871 454518014 0.000000e+00 2861.0
8 TraesCS4D01G215400 chr4B 89.186 786 45 19 4841 5593 454518010 454518788 0.000000e+00 944.0
9 TraesCS4D01G215400 chr4B 92.181 243 15 3 5718 5959 454518986 454519225 2.190000e-89 340.0
10 TraesCS4D01G215400 chr4B 89.219 269 23 3 5983 6247 454519340 454519606 1.320000e-86 331.0
11 TraesCS4D01G215400 chr4B 92.806 139 10 0 2559 2697 454515694 454515832 1.080000e-47 202.0
12 TraesCS4D01G215400 chr7A 80.759 395 45 15 5785 6155 205112898 205112511 4.850000e-71 279.0
13 TraesCS4D01G215400 chr2B 80.645 403 39 17 5785 6153 780870042 780869645 6.280000e-70 276.0
14 TraesCS4D01G215400 chr5D 80.201 399 41 18 5785 6153 368032828 368032438 1.360000e-66 265.0
15 TraesCS4D01G215400 chr5D 79.208 404 43 17 5785 6151 63154586 63154985 6.370000e-60 243.0
16 TraesCS4D01G215400 chr5A 79.899 398 42 18 5785 6153 470079887 470079499 2.270000e-64 257.0
17 TraesCS4D01G215400 chr5A 81.350 311 32 15 5785 6073 184259616 184259310 4.960000e-56 230.0
18 TraesCS4D01G215400 chr5B 79.064 406 41 17 5785 6153 436099192 436098794 8.240000e-59 239.0
19 TraesCS4D01G215400 chr5B 75.743 404 40 18 5785 6153 436156719 436156339 3.970000e-32 150.0
20 TraesCS4D01G215400 chr5B 83.051 118 13 6 408 522 6538484 6538597 4.050000e-17 100.0
21 TraesCS4D01G215400 chr7D 80.656 305 37 14 5785 6070 554556468 554556769 3.860000e-52 217.0
22 TraesCS4D01G215400 chr7D 79.000 300 43 13 5870 6153 384020347 384020642 3.030000e-43 187.0
23 TraesCS4D01G215400 chr2D 77.887 407 49 18 5785 6153 605780020 605779617 1.390000e-51 215.0
24 TraesCS4D01G215400 chr3A 82.895 228 35 3 318 542 652576653 652576879 1.080000e-47 202.0
25 TraesCS4D01G215400 chr3A 82.895 228 35 3 318 542 652664835 652665061 1.080000e-47 202.0
26 TraesCS4D01G215400 chr3A 82.895 228 34 4 318 542 652711199 652711424 3.890000e-47 200.0
27 TraesCS4D01G215400 chr1B 81.893 243 38 5 309 547 525831734 525831494 3.890000e-47 200.0
28 TraesCS4D01G215400 chr1B 83.333 126 20 1 413 537 591353667 591353542 1.450000e-21 115.0
29 TraesCS4D01G215400 chr1B 80.851 141 24 3 408 546 470551186 470551047 2.420000e-19 108.0
30 TraesCS4D01G215400 chr3D 76.538 439 55 25 5757 6153 544821239 544820807 5.030000e-46 196.0
31 TraesCS4D01G215400 chr3D 82.394 142 18 5 408 545 523941812 523941674 4.030000e-22 117.0
32 TraesCS4D01G215400 chr1D 76.647 334 39 15 5858 6153 2108102 2107770 1.430000e-31 148.0
33 TraesCS4D01G215400 chr1A 78.571 154 13 9 5925 6058 336872869 336872716 4.080000e-12 84.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G215400 chr4D 369111581 369117936 6355 False 11738.000000 11738 100.0000 1 6356 1 chr4D.!!$F1 6355
1 TraesCS4D01G215400 chr4A 95376748 95383343 6595 True 2397.000000 4700 91.6500 2 6356 4 chr4A.!!$R1 6354
2 TraesCS4D01G215400 chr4B 454513031 454519606 6575 False 1284.166667 3027 90.6205 71 6247 6 chr4B.!!$F1 6176

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
570 626 0.033796 ACCTTGGGAGCACATGATGG 60.034 55.000 0.00 0.00 0.00 3.51 F
707 790 0.036388 GCCTCCCATCAACTCAACGA 60.036 55.000 0.00 0.00 0.00 3.85 F
991 1098 1.127343 ATACAGAGGGAAGGAGCAGC 58.873 55.000 0.00 0.00 0.00 5.25 F
1218 1338 1.377725 CCCCATGACGCTGCTCTTT 60.378 57.895 0.00 0.00 0.00 2.52 F
1446 1566 1.445582 CTGACTAACCGTCCGTGCC 60.446 63.158 0.00 0.00 42.13 5.01 F
2752 3065 1.830477 GACTTTTGGGGGCATGCATAA 59.170 47.619 21.36 5.56 0.00 1.90 F
3773 4216 1.067516 GCATGGCCATGTCATGTAACC 59.932 52.381 39.08 20.21 46.06 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 2069 1.956043 GCCAACGGCTGAAATGACA 59.044 52.632 0.00 0.00 46.69 3.58 R
2492 2625 2.021457 AGGGTGTACAAAACAGTGTGC 58.979 47.619 0.00 0.00 39.29 4.57 R
2966 3280 0.320374 AAATGGAAGGTCACGCGAGA 59.680 50.000 15.93 7.99 0.00 4.04 R
3047 3361 0.823356 AGCACGGCAATTGGTGTTCT 60.823 50.000 7.72 0.00 36.54 3.01 R
3511 3829 4.201910 CCAGCGTAAGTGATTGGTAATTGG 60.202 45.833 0.00 0.00 41.68 3.16 R
3813 4256 0.960861 GGGAGTGCAGTACCCTTTGC 60.961 60.000 12.35 0.00 40.39 3.68 R
5383 5961 0.399454 AGCAGCATGAGACACTTGGT 59.601 50.000 0.00 0.00 39.69 3.67 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 174 2.930826 AACGGTCAAGGAAGACATGT 57.069 45.000 0.00 0.00 40.29 3.21
346 377 6.723131 ACTTTAGGTCGAAACTCTAAATGC 57.277 37.500 10.07 0.00 32.54 3.56
348 379 6.879458 ACTTTAGGTCGAAACTCTAAATGCAT 59.121 34.615 0.00 0.00 32.54 3.96
435 469 9.906660 TGACACTATTCACATTTAAATTTGTCC 57.093 29.630 12.78 0.00 31.77 4.02
485 520 6.140377 AGTTTGGACCTGAAATTTTTAGGGA 58.860 36.000 20.45 5.13 35.89 4.20
491 526 7.898636 TGGACCTGAAATTTTTAGGGATTGTAT 59.101 33.333 20.45 1.78 35.89 2.29
564 620 0.615331 GAGATCACCTTGGGAGCACA 59.385 55.000 0.00 0.00 0.00 4.57
568 624 0.994247 TCACCTTGGGAGCACATGAT 59.006 50.000 0.00 0.00 0.00 2.45
569 625 1.100510 CACCTTGGGAGCACATGATG 58.899 55.000 0.00 0.00 0.00 3.07
570 626 0.033796 ACCTTGGGAGCACATGATGG 60.034 55.000 0.00 0.00 0.00 3.51
578 634 2.549754 GGAGCACATGATGGTATTTCCG 59.450 50.000 0.00 0.00 39.82 4.30
579 635 2.549754 GAGCACATGATGGTATTTCCGG 59.450 50.000 0.00 0.00 39.82 5.14
580 636 2.092429 AGCACATGATGGTATTTCCGGT 60.092 45.455 0.00 0.00 37.23 5.28
581 637 3.135712 AGCACATGATGGTATTTCCGGTA 59.864 43.478 0.00 0.00 37.23 4.02
582 638 3.498397 GCACATGATGGTATTTCCGGTAG 59.502 47.826 0.00 0.00 39.52 3.18
586 642 4.942761 TGATGGTATTTCCGGTAGGTAC 57.057 45.455 0.00 0.00 39.52 3.34
596 678 1.105457 CGGTAGGTACGGATGGTTGA 58.895 55.000 0.00 0.00 0.00 3.18
602 684 4.829872 AGGTACGGATGGTTGAACATAA 57.170 40.909 0.00 0.00 0.00 1.90
700 783 1.450312 CACGAGGCCTCCCATCAAC 60.450 63.158 27.20 0.00 0.00 3.18
705 788 0.329596 AGGCCTCCCATCAACTCAAC 59.670 55.000 0.00 0.00 0.00 3.18
706 789 1.026718 GGCCTCCCATCAACTCAACG 61.027 60.000 0.00 0.00 0.00 4.10
707 790 0.036388 GCCTCCCATCAACTCAACGA 60.036 55.000 0.00 0.00 0.00 3.85
708 791 1.610624 GCCTCCCATCAACTCAACGAA 60.611 52.381 0.00 0.00 0.00 3.85
709 792 2.778299 CCTCCCATCAACTCAACGAAA 58.222 47.619 0.00 0.00 0.00 3.46
711 794 3.189287 CCTCCCATCAACTCAACGAAAAG 59.811 47.826 0.00 0.00 0.00 2.27
712 795 4.065088 CTCCCATCAACTCAACGAAAAGA 58.935 43.478 0.00 0.00 0.00 2.52
713 796 4.456535 TCCCATCAACTCAACGAAAAGAA 58.543 39.130 0.00 0.00 0.00 2.52
714 797 4.274950 TCCCATCAACTCAACGAAAAGAAC 59.725 41.667 0.00 0.00 0.00 3.01
715 798 4.275936 CCCATCAACTCAACGAAAAGAACT 59.724 41.667 0.00 0.00 0.00 3.01
716 799 5.207768 CCATCAACTCAACGAAAAGAACTG 58.792 41.667 0.00 0.00 0.00 3.16
717 800 5.220854 CCATCAACTCAACGAAAAGAACTGT 60.221 40.000 0.00 0.00 0.00 3.55
718 801 5.873179 TCAACTCAACGAAAAGAACTGTT 57.127 34.783 0.00 0.00 0.00 3.16
719 802 6.249035 TCAACTCAACGAAAAGAACTGTTT 57.751 33.333 0.00 0.00 0.00 2.83
720 803 6.674066 TCAACTCAACGAAAAGAACTGTTTT 58.326 32.000 0.00 0.00 32.18 2.43
721 804 6.799925 TCAACTCAACGAAAAGAACTGTTTTC 59.200 34.615 0.00 2.75 41.24 2.29
800 891 5.050227 CACAAATACGACCGGACACTTAAAA 60.050 40.000 9.46 0.00 0.00 1.52
802 893 5.596268 AATACGACCGGACACTTAAAAAC 57.404 39.130 9.46 0.00 0.00 2.43
803 894 2.212652 ACGACCGGACACTTAAAAACC 58.787 47.619 9.46 0.00 0.00 3.27
991 1098 1.127343 ATACAGAGGGAAGGAGCAGC 58.873 55.000 0.00 0.00 0.00 5.25
1026 1137 3.393970 CCTGGGCCTCTCGCTTCA 61.394 66.667 4.53 0.00 37.74 3.02
1218 1338 1.377725 CCCCATGACGCTGCTCTTT 60.378 57.895 0.00 0.00 0.00 2.52
1248 1368 4.980805 TTCTGCGCCCGCTTCGTT 62.981 61.111 14.13 0.00 42.51 3.85
1277 1397 2.098770 GCCTACTGTACAAGGTACGGAG 59.901 54.545 19.22 11.24 35.16 4.63
1446 1566 1.445582 CTGACTAACCGTCCGTGCC 60.446 63.158 0.00 0.00 42.13 5.01
1944 2069 7.176515 TCTGATGTTTGGCTGTTTGTATATGTT 59.823 33.333 0.00 0.00 0.00 2.71
1945 2070 7.089538 TGATGTTTGGCTGTTTGTATATGTTG 58.910 34.615 0.00 0.00 0.00 3.33
1946 2071 6.398234 TGTTTGGCTGTTTGTATATGTTGT 57.602 33.333 0.00 0.00 0.00 3.32
2492 2625 6.711194 TGTATCCTCTCCTTCACGAGTATTAG 59.289 42.308 0.00 0.00 0.00 1.73
2503 2636 5.294356 TCACGAGTATTAGCACACTGTTTT 58.706 37.500 0.00 0.00 0.00 2.43
2554 2771 4.943705 ACCATTATCTTGTACTGGCACTTG 59.056 41.667 0.00 0.00 0.00 3.16
2578 2891 7.424803 TGGAGGAAATATTTATGCACATTTCG 58.575 34.615 0.00 0.00 37.96 3.46
2653 2966 7.229581 AGTCAAGAAAGTTAGGTAGATTCGT 57.770 36.000 0.00 0.00 0.00 3.85
2699 3012 5.194432 TGTTACTGTCTCATAGAGAGTCCC 58.806 45.833 9.72 3.80 44.42 4.46
2741 3054 9.981114 AATAACTTGAAATAACTGACTTTTGGG 57.019 29.630 0.00 0.00 0.00 4.12
2752 3065 1.830477 GACTTTTGGGGGCATGCATAA 59.170 47.619 21.36 5.56 0.00 1.90
2966 3280 5.255443 AGGAAATGTGAGGGGTAAGGTTTAT 59.745 40.000 0.00 0.00 0.00 1.40
3007 3321 2.703007 AGAGGGGAAGATGCATACTCAC 59.297 50.000 0.00 0.00 0.00 3.51
3040 3354 9.081997 GTTCTTTGTTTGTTGTTTGATGACATA 57.918 29.630 0.00 0.00 0.00 2.29
3047 3361 6.572167 TGTTGTTTGATGACATAATGCTCA 57.428 33.333 0.00 0.00 0.00 4.26
3488 3806 8.084985 TGATGTGTCCTATTTATGGTCAGTTA 57.915 34.615 0.00 0.00 0.00 2.24
3773 4216 1.067516 GCATGGCCATGTCATGTAACC 59.932 52.381 39.08 20.21 46.06 2.85
3813 4256 8.456471 TCTGAAAATCATTGTGCTTCATTAGAG 58.544 33.333 0.00 0.00 0.00 2.43
3846 4289 4.724399 TGCACTCCCTTCTTGTAATTTCA 58.276 39.130 0.00 0.00 0.00 2.69
3876 4323 3.504520 TCATGCAGCATGGCTATGTAATG 59.495 43.478 30.92 6.70 41.66 1.90
4242 4692 4.193090 TCAAGGTTCGTTTGCTACTTTGA 58.807 39.130 0.00 0.00 36.10 2.69
4519 4974 6.647895 AGGTTTTATTTCTTTGCTGCAATCAG 59.352 34.615 16.77 11.63 43.16 2.90
4668 5131 7.552687 CCAGATAATACAGGCTTAACTTTGTCA 59.447 37.037 0.00 0.00 0.00 3.58
4702 5186 4.634012 TTTCGAAATGAAAGGAGAGGGA 57.366 40.909 6.47 0.00 41.59 4.20
4799 5283 8.388853 GCATGAATAGTGCAGTCATAATATCAG 58.611 37.037 0.00 0.00 39.89 2.90
4821 5305 9.809395 ATCAGACATTGATCAGATTGGATAATT 57.191 29.630 0.00 0.00 43.03 1.40
5006 5570 4.359706 GGTGGTTCTTTGACAATTGTGAC 58.640 43.478 17.58 2.76 0.00 3.67
5045 5609 2.853235 ACCTTGCCCTGTACTTACAC 57.147 50.000 0.00 0.00 31.93 2.90
5146 5711 2.173569 AGACCAAGAAACAGAGCAGGTT 59.826 45.455 0.00 0.00 0.00 3.50
5256 5821 2.367567 AGAGGTCGTTTTCTGTGGCTTA 59.632 45.455 0.00 0.00 0.00 3.09
5292 5857 4.709397 AGAAACTCCTCTCTACCATGTCTG 59.291 45.833 0.00 0.00 0.00 3.51
5306 5871 4.686972 CCATGTCTGGTATACTGTGACTG 58.313 47.826 17.39 13.97 37.79 3.51
5375 5953 5.078411 TCAGGAGCTTAGAAATCTCACAC 57.922 43.478 0.00 0.00 0.00 3.82
5383 5961 6.155221 AGCTTAGAAATCTCACACCTGATGTA 59.845 38.462 0.00 0.00 40.64 2.29
5431 6009 3.194062 ACTTTTTGACGGCATTGGTTTG 58.806 40.909 0.00 0.00 0.00 2.93
5435 6013 1.234821 TGACGGCATTGGTTTGTCTC 58.765 50.000 0.00 0.00 0.00 3.36
5436 6014 0.521735 GACGGCATTGGTTTGTCTCC 59.478 55.000 0.00 0.00 0.00 3.71
5458 6050 7.173390 TCTCCTTATCTATGTGTGACTACGATG 59.827 40.741 0.00 0.00 0.00 3.84
5514 6114 6.306837 CGTGTTGTTAAGAGAGTTCTGAGATC 59.693 42.308 0.00 0.00 32.79 2.75
5547 6147 1.258676 CTAGGGAGTTAGGGATCCGC 58.741 60.000 5.45 0.00 36.38 5.54
5576 6176 3.554934 TGTCAAGCTTTGTTCTGGTGAT 58.445 40.909 0.00 0.00 0.00 3.06
5622 6222 4.637534 GCAGGATGTCTAGATGAGCAAAAA 59.362 41.667 0.00 0.00 39.31 1.94
5669 6269 8.433421 TTTCTTCACTCTAACTTGATTTCGTT 57.567 30.769 0.00 0.00 0.00 3.85
5869 6632 7.271511 ACTTTGCAGTTTCAAAACATTATGGA 58.728 30.769 8.23 0.00 41.30 3.41
5903 6666 7.864686 CACATGTATACAAGGATGTAATGTGG 58.135 38.462 10.14 0.00 44.99 4.17
6058 6916 9.554724 CTGGAAATTTACACACATGTACATTAC 57.445 33.333 5.37 0.00 39.63 1.89
6121 6979 4.403734 TGAAGTTTCCGAATTAAGGCCTT 58.596 39.130 24.18 24.18 0.00 4.35
6151 7009 2.491693 TCGGTCTCCATTTGGCATTTTC 59.508 45.455 0.00 0.00 34.44 2.29
6198 7058 6.181190 TGTTACCAAACCCGATATTTCATGA 58.819 36.000 0.00 0.00 34.49 3.07
6200 7060 7.340743 TGTTACCAAACCCGATATTTCATGATT 59.659 33.333 0.00 0.00 34.49 2.57
6212 7072 7.430211 CGATATTTCATGATTGGTTGTGTCTTG 59.570 37.037 0.00 0.00 0.00 3.02
6257 7117 8.831550 CCAAAGTTTAATAGTAGAGGCATCTTC 58.168 37.037 6.05 0.31 36.96 2.87
6279 7139 9.903682 TCTTCATTTTCTTATCTTGCTCTTTTG 57.096 29.630 0.00 0.00 0.00 2.44
6309 7169 5.078411 ACTTTAGCAGAGTCACCATAGTG 57.922 43.478 0.00 0.00 46.00 2.74
6312 7172 0.179000 GCAGAGTCACCATAGTGGGG 59.821 60.000 0.52 0.00 44.11 4.96
6314 7174 1.482593 CAGAGTCACCATAGTGGGGTC 59.517 57.143 0.00 0.00 42.97 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 6.013553 GGAGGATTCCTTCCCCTATAGTTTAC 60.014 46.154 6.68 0.00 46.81 2.01
49 50 2.528813 TCTGGAGGATTCCTTCCCCTAT 59.471 50.000 8.61 0.00 46.81 2.57
53 54 2.681097 CGTTTCTGGAGGATTCCTTCCC 60.681 54.545 8.61 6.05 46.81 3.97
55 56 3.611766 TCGTTTCTGGAGGATTCCTTC 57.388 47.619 6.68 5.18 44.36 3.46
59 60 7.553881 TTTTATGATCGTTTCTGGAGGATTC 57.446 36.000 0.00 0.00 0.00 2.52
67 68 9.778993 ATGAGTTCATTTTTATGATCGTTTCTG 57.221 29.630 0.00 0.00 31.37 3.02
143 174 1.067425 AGTAGTTTGCGTGCACGGATA 60.067 47.619 37.47 28.41 39.94 2.59
198 229 1.003118 TGTTTGTCTAGCCTTCGCCAT 59.997 47.619 0.00 0.00 34.57 4.40
276 307 5.121454 GCCACTGATTTGTCTCTAGAAGTTG 59.879 44.000 0.00 0.00 0.00 3.16
327 358 5.730550 ACATGCATTTAGAGTTTCGACCTA 58.269 37.500 0.00 0.00 0.00 3.08
328 359 4.579869 ACATGCATTTAGAGTTTCGACCT 58.420 39.130 0.00 0.00 0.00 3.85
447 482 6.642950 CAGGTCCAAACTCGAGATATACATTC 59.357 42.308 21.68 0.92 0.00 2.67
454 489 5.677319 ATTTCAGGTCCAAACTCGAGATA 57.323 39.130 21.68 0.00 0.00 1.98
457 492 5.438761 AAAATTTCAGGTCCAAACTCGAG 57.561 39.130 11.84 11.84 0.00 4.04
533 573 6.442112 CCAAGGTGATCTCTTGAAAAGTTTC 58.558 40.000 22.27 0.00 46.34 2.78
542 582 1.280133 TGCTCCCAAGGTGATCTCTTG 59.720 52.381 16.99 16.99 40.75 3.02
545 585 0.615331 TGTGCTCCCAAGGTGATCTC 59.385 55.000 0.00 0.00 0.00 2.75
546 586 1.064906 CATGTGCTCCCAAGGTGATCT 60.065 52.381 0.00 0.00 0.00 2.75
549 589 0.994247 ATCATGTGCTCCCAAGGTGA 59.006 50.000 0.00 0.00 0.00 4.02
550 590 1.100510 CATCATGTGCTCCCAAGGTG 58.899 55.000 0.00 0.00 0.00 4.00
552 592 0.033796 ACCATCATGTGCTCCCAAGG 60.034 55.000 0.00 0.00 0.00 3.61
553 593 2.715749 TACCATCATGTGCTCCCAAG 57.284 50.000 0.00 0.00 0.00 3.61
554 594 3.668141 AATACCATCATGTGCTCCCAA 57.332 42.857 0.00 0.00 0.00 4.12
564 620 4.021719 CGTACCTACCGGAAATACCATCAT 60.022 45.833 9.46 0.00 38.90 2.45
578 634 2.234414 TGTTCAACCATCCGTACCTACC 59.766 50.000 0.00 0.00 0.00 3.18
579 635 3.598019 TGTTCAACCATCCGTACCTAC 57.402 47.619 0.00 0.00 0.00 3.18
580 636 5.422970 ACTTATGTTCAACCATCCGTACCTA 59.577 40.000 0.00 0.00 0.00 3.08
581 637 4.224370 ACTTATGTTCAACCATCCGTACCT 59.776 41.667 0.00 0.00 0.00 3.08
582 638 4.510571 ACTTATGTTCAACCATCCGTACC 58.489 43.478 0.00 0.00 0.00 3.34
624 706 2.050442 GTTCCGCTTTTGCCACCG 60.050 61.111 0.00 0.00 43.93 4.94
631 713 2.545742 GCTGATGGTTTGTTCCGCTTTT 60.546 45.455 0.00 0.00 0.00 2.27
729 812 9.713713 GACTAATTAAGACTCCAGTTCTTCTTT 57.286 33.333 0.00 0.00 30.89 2.52
730 813 8.315482 GGACTAATTAAGACTCCAGTTCTTCTT 58.685 37.037 0.00 0.00 32.99 2.52
732 815 7.612677 TGGACTAATTAAGACTCCAGTTCTTC 58.387 38.462 0.00 0.00 29.33 2.87
733 816 7.310734 CCTGGACTAATTAAGACTCCAGTTCTT 60.311 40.741 18.22 0.00 42.83 2.52
734 817 6.155393 CCTGGACTAATTAAGACTCCAGTTCT 59.845 42.308 18.22 0.00 42.83 3.01
735 818 6.154706 TCCTGGACTAATTAAGACTCCAGTTC 59.845 42.308 18.22 1.53 42.83 3.01
736 819 6.023603 TCCTGGACTAATTAAGACTCCAGTT 58.976 40.000 18.22 0.00 42.83 3.16
800 891 3.473625 AGAATTTCGTCGTCTTTGGGTT 58.526 40.909 0.00 0.00 0.00 4.11
802 893 3.617263 CCTAGAATTTCGTCGTCTTTGGG 59.383 47.826 0.00 0.00 0.00 4.12
803 894 3.617263 CCCTAGAATTTCGTCGTCTTTGG 59.383 47.826 0.00 0.00 0.00 3.28
1024 1135 3.319198 GCGGTTGAGGAGGGGTGA 61.319 66.667 0.00 0.00 0.00 4.02
1026 1137 4.658786 AGGCGGTTGAGGAGGGGT 62.659 66.667 0.00 0.00 0.00 4.95
1218 1338 1.296715 GCAGAAGAAGCCGAGGGAA 59.703 57.895 0.00 0.00 0.00 3.97
1248 1368 0.036105 TGTACAGTAGGCGGTCGAGA 60.036 55.000 0.00 0.00 0.00 4.04
1446 1566 2.491152 GGGCGTTGCATCACATGG 59.509 61.111 0.00 0.00 0.00 3.66
1944 2069 1.956043 GCCAACGGCTGAAATGACA 59.044 52.632 0.00 0.00 46.69 3.58
1945 2070 4.868195 GCCAACGGCTGAAATGAC 57.132 55.556 0.00 0.00 46.69 3.06
2492 2625 2.021457 AGGGTGTACAAAACAGTGTGC 58.979 47.619 0.00 0.00 39.29 4.57
2524 2741 6.700520 GCCAGTACAAGATAATGGTACAGTAC 59.299 42.308 1.59 1.59 43.30 2.73
2554 2771 7.425606 ACGAAATGTGCATAAATATTTCCTCC 58.574 34.615 3.39 0.00 36.61 4.30
2735 3048 2.641815 ACTTTTATGCATGCCCCCAAAA 59.358 40.909 16.68 13.89 0.00 2.44
2752 3065 8.193438 GCTGGATAATAGATTCTTTGCAACTTT 58.807 33.333 0.00 0.00 0.00 2.66
2765 3078 5.717178 AGTATGTGGTCGCTGGATAATAGAT 59.283 40.000 0.00 0.00 0.00 1.98
2966 3280 0.320374 AAATGGAAGGTCACGCGAGA 59.680 50.000 15.93 7.99 0.00 4.04
3007 3321 2.399396 ACAAACAAAGAACGGCATCG 57.601 45.000 0.00 0.00 43.02 3.84
3040 3354 2.028748 GGCAATTGGTGTTCTGAGCATT 60.029 45.455 7.72 0.00 0.00 3.56
3047 3361 0.823356 AGCACGGCAATTGGTGTTCT 60.823 50.000 7.72 0.00 36.54 3.01
3511 3829 4.201910 CCAGCGTAAGTGATTGGTAATTGG 60.202 45.833 0.00 0.00 41.68 3.16
3813 4256 0.960861 GGGAGTGCAGTACCCTTTGC 60.961 60.000 12.35 0.00 40.39 3.68
3895 4342 8.893219 TGCCTCTATAGTACAATGATTTTCAG 57.107 34.615 0.00 0.00 0.00 3.02
3896 4343 9.851686 AATGCCTCTATAGTACAATGATTTTCA 57.148 29.630 0.00 0.00 0.00 2.69
3898 4345 9.851686 TGAATGCCTCTATAGTACAATGATTTT 57.148 29.630 0.00 0.00 0.00 1.82
4060 4510 1.253116 CGTCATGCAACGCAAGAATG 58.747 50.000 0.00 0.00 43.62 2.67
4228 4678 9.988350 AGAAATTATGTATCAAAGTAGCAAACG 57.012 29.630 0.00 0.00 0.00 3.60
4519 4974 5.500825 GGTGAATGCAAATCAAACAACAAC 58.499 37.500 7.09 0.00 0.00 3.32
4668 5131 6.018098 TTTCATTTCGAAATGCACAATTTGCT 60.018 30.769 35.42 6.04 44.27 3.91
4816 5300 3.764237 ATCGGAGCCGGTTACAATTAT 57.236 42.857 9.29 0.00 40.25 1.28
4821 5305 1.405872 ATGTATCGGAGCCGGTTACA 58.594 50.000 19.95 19.95 40.09 2.41
5006 5570 1.216178 CCAGCAAAGAAATGGCCCG 59.784 57.895 0.00 0.00 0.00 6.13
5045 5609 2.346803 CCGACCAACACAATCTACTGG 58.653 52.381 0.00 0.00 0.00 4.00
5118 5682 5.178797 GCTCTGTTTCTTGGTCTAGCAATA 58.821 41.667 0.00 0.00 0.00 1.90
5146 5711 8.211030 TGCTAGCTATACCCGGTATATATAGA 57.789 38.462 24.49 14.73 32.74 1.98
5256 5821 4.100373 AGGAGTTTCTAAGCTCTGTGGAT 58.900 43.478 6.54 0.00 36.61 3.41
5292 5857 4.948621 ACCTACTCACAGTCACAGTATACC 59.051 45.833 0.00 0.00 0.00 2.73
5306 5871 9.099454 CCATGAATTAGAACTAAACCTACTCAC 57.901 37.037 0.00 0.00 0.00 3.51
5368 5933 3.006859 CACTTGGTACATCAGGTGTGAGA 59.993 47.826 0.00 0.00 42.24 3.27
5369 5934 3.329386 CACTTGGTACATCAGGTGTGAG 58.671 50.000 0.00 0.00 42.24 3.51
5375 5953 3.961480 TGAGACACTTGGTACATCAGG 57.039 47.619 0.00 0.00 39.30 3.86
5383 5961 0.399454 AGCAGCATGAGACACTTGGT 59.601 50.000 0.00 0.00 39.69 3.67
5431 6009 6.482641 TCGTAGTCACACATAGATAAGGAGAC 59.517 42.308 0.00 0.00 0.00 3.36
5435 6013 6.382608 CCATCGTAGTCACACATAGATAAGG 58.617 44.000 0.00 0.00 0.00 2.69
5436 6014 5.859114 GCCATCGTAGTCACACATAGATAAG 59.141 44.000 0.00 0.00 0.00 1.73
5458 6050 5.846203 ACATTATAAACCAATGCAGATGCC 58.154 37.500 1.72 0.00 41.18 4.40
5547 6147 6.312487 CAGAACAAAGCTTGACATGTCTATG 58.688 40.000 25.55 15.38 40.24 2.23
5576 6176 3.057104 CCTGTCAGCATCTGAAATTGCAA 60.057 43.478 0.00 0.00 42.46 4.08
5622 6222 1.575419 TAGCAAACCCACCCGTAGAT 58.425 50.000 0.00 0.00 0.00 1.98
5669 6269 3.118884 GGGATCCGTCTTACAAGCACTTA 60.119 47.826 5.45 0.00 0.00 2.24
5903 6666 6.326375 TCATCCCAAAATTTTACGCACATAC 58.674 36.000 2.44 0.00 0.00 2.39
6021 6879 8.138712 GTGTGTAAATTTCCAGGTCAAAATACA 58.861 33.333 0.00 0.00 0.00 2.29
6091 6949 8.915654 CCTTAATTCGGAAACTTCAAAATTCAG 58.084 33.333 0.00 4.83 30.54 3.02
6151 7009 1.808411 ATGTAGCACCAAGTTGTCCG 58.192 50.000 1.45 0.00 0.00 4.79
6198 7058 7.707624 ACATGATATTCAAGACACAACCAAT 57.292 32.000 0.00 0.00 0.00 3.16
6200 7060 8.806429 ATAACATGATATTCAAGACACAACCA 57.194 30.769 0.00 0.00 0.00 3.67
6279 7139 4.623595 GTGACTCTGCTAAAGTTGCTCTAC 59.376 45.833 0.00 0.00 0.00 2.59
6291 7151 2.388735 CCCACTATGGTGACTCTGCTA 58.611 52.381 11.31 0.00 45.61 3.49
6309 7169 4.603946 GTATGGAGCGGCGACCCC 62.604 72.222 12.98 8.50 0.00 4.95
6322 7182 3.753272 CCAATAGCCTCCAAATCCGTATG 59.247 47.826 0.00 0.00 0.00 2.39


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.